SortBam

Overview

Group: SAM/BAM

Sorts a SAM or BAM file. Several sort orders are available:

1. Coordinate: sorts reads by their reference sequence and left-most aligned coordinate
2. Queryname: sort the reads by their query (i.e. read) name
3. Random: sorts the reads into a random order. The output is deterministic for any given input. and several
4. RandomQuery: sorts the reads into a random order but keeps reads with the same queryname together. The ordering is deterministic for any given input.

Uses a temporary directory to buffer sets of sorted reads to disk. The number of reads kept in memory affects memory use and can be changed with the --max-records-in-ram option. The temporary directory to use can be set with the fgbio global option --tmp-dir.

An example invocation might look like:

java -Xmx4g -jar fgbio.jar --tmp-dir=/my/big/scratch/volume \
  SortBam --input=queryname.bam --sort-order=Coordinate --output coordinate.bam

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToBam	Input SAM or BAM.	Required	1
output	o	PathToBam	Output SAM or BAM.	Required	1
sort-order	s	SamOrder	Order into which to sort the records.	Optional	1	Coordinate
max-records-in-ram	m	Int	Max records in RAM.	Optional	1	1000000